Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock ...species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (F
), genomic relationship matrix approach (F
) and based on the observed versus expected number of homozygous genotypes (F
), and from pedigree-based coefficient (F
).
ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH
) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of F
, F
, F
, and F
approaches. F
estimates ranged from 0.00 to 0.327 and F
from 0.001 to 0.201. Low to moderate correlations were observed between F
-F
and F
-F
, with values ranging from -0.11 to 0.51. Low to high correlations were observed between F
-F
and moderate between F
-F
and F
-F
. Correlations between F
from different lengths and F
gradually increased with ROH length.
Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low F
F
correlations for small segments indicate that F
estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that F
can be used as an alternative to inbreeding estimates in the absence of pedigree records.
Further characterization of genetic structural variations should strongly focus on small and endangered local breeds given their role in unraveling genes and structural variants underlying selective ...pressures and phenotype variation. A comprehensive genome‐wide assessment of copy number variations (CNVs) based on whole‐genome re‐sequencing data was performed on three Brazilian locally adapted cattle breeds (Caracu Caldeano, Crioulo Lageano, and Pantaneiro) using the ARS‐UCD1.2 genome assembly. Data from 36 individuals with an average coverage depth of 14.07× per individual was used. A total of 24 945 CNVs were identified distributed among the breeds (Caracu Caldeano = 7285, Crioulo Lageano = 7297, and Pantaneiro = 10 363). Deletion events were 1.75–2.07‐fold higher than duplications, and the total length of CNVs is composed mostly of a high number of segments between 10 and 30 kb. CNV regions (CNVRs) are not uniformly scattered throughout the genomes (n = 463), and 105 CNVRs were found overlapping among the studied breeds. Functional annotation of the CNVRs revealed variants with high consequence on protein sequence harboring relevant genes, in which we highlighted the BOLA‐DQB, BOLA‐DQA5, CD1A, β‐defensins, PRG3, and ULBP21 genes. Enrichment analysis based on the gene list retrieved from the CNVRs disclosed over‐represented terms (p < 0.01) strongly associated with immunity and cattle resilience to harsh environments. Additionally, QTL associated with body conformation and dairy‐related traits were also unveiled within the CNVRs. These results provide better understanding of the selective forces shaping the genome of such cattle breeds and identify traces of natural selection pressures by which these populations have been exposed to challenging environmental conditions.
The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to ...the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics.
A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations' historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds.
The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions.
ABSTRACT The objective of this study was to investigate changes in physiological parameters of dairy cows and understand which physiological parameters show greater reliability for verification of ...heat stress. Blood samples were collected for analysis and included hematocrit (Ht), erythrocyte count (ERY), and hemoglobin count (HEMO). In addition, physiological variables, including rectal temperature (RT), heart rate (HR), respiratory rate (RR), and panting score (PS) were recorded in 38 lactating cows. These varied according to genetic group (1/2, 3/4, and pure bred Holstein (HO)). Analysis of variance considering the effects of genetic group, days, and their interaction as well as linear and quadratic effect of the black globe humidity index (BGHI) was performed, as well as broken-line regression. These values were higher in pure HO than in 3/4 and 1/2 groups. The average BGHI during the morning was 74, when 70, 43, and 13% of pure HO, 3/4, and 1/2, respectively, presented RR above reference value. The RR was the best indicator of heat stress and its critical value was 116 breaths/min for 1/2, 140 for 3/4, and 168 breaths/min for pure HO cows. In the HO group, physiological variables increased linearly with BGHI, without presenting inflection in the regression. The inflection point occurred at a higher BGHI for the 1/2 group compared with the other groups. Hematocrit and HEMO were different among genetic groups and did not vary with BGHI, showing that stress was not sufficient to alter these hematological parameters. The 1/2 HO group was capable of maintaining normal physiological parameters for at least 3 BGHI units above that of HO and 1 to 3 units higher than 3/4 HO for RR and RT, respectively. Respiratory rate is the physiological parameter that best predicts heat stress in dairy cattle, and the 1/2 Holstein group is the best adapted to heat stress.
ABSTRACT The objective of this study was to determine whether infrared thermography is a useful tool for the recognition of dairy cows in a state of thermal heat stress, as well as to identify the ...best region of the animal to be evaluated for this recognition. Physiological variables, including rectal temperature, respiratory frequency, cardiac frequency, and panting score were recorded in 38 lactating cows. For the assessment of environmental parameters, a digital black globe thermometer (TGD-200 model) was used. Thermographic photographs of different regions of the body of cows were taken using an infrared camera (FLIR® System T300) and indicated respective superficial temperature. Physiological variables and superficial body temperature in different regions varied between genetic groups (Girolando: ½ Holstein × ½ Gir and ¾ Holstein × ¼ Gir; purebred Holstein). The environmental temperature ranged from 20.7 to 37.9 °C with a relative humidity reaching 95%. The mean rectal temperature (40.84 °C), respiratory frequency (111.36 breaths/min), and cardiac frequency (99.22 beats/min) were higher for pure Holstein than for Girolando cows. Positive correlations were found between the physiological parameters and thermographic measures. The highest positive correlation (0.74) was found between the temperature in the lateral region of the udder and rectal temperature. Thermography is a good indicator of thermal comfort. The best region to identify heat stress in cows using thermography is the lateral region of the udder.
Host resilience (HR) to parasites can affect the performance of animals. Therefore, the aim of this study was to present a detailed investigation of the genetic mechanisms of HR to ticks (TICK), ...gastrointestinal nematodes (GIN), and Eimeria spp. (EIM) in Nellore cattle that were raised under natural infestation and a prophylactic parasite control strategy. In our study, HR was defined as the slope coefficient of body weight (BW) when TICK, GIN, and EIM burdens were used as environmental gradients in random regression models. In total, 1712 animals were evaluated at five measurement events (ME) at an average age of 331, 385, 443, 498, and 555 days, which generated 7307 body weight (BW) records. Of the 1712 animals, 1075 genotyped animals were used in genome-wide association studies to identify genomic regions associated with HR. Posterior means of the heritability estimates for BW ranged from 0.09 to 0.54 across parasites and ME. The single nucleotide polymorphism (SNP)-derived heritability for BW at each ME ranged from a low (0.09 at ME.331) to a moderate value (0.23 at ME.555). Those estimates show that genetic progress can be achieved for BW through selection. Both genetic and genomic associations between BW and HR to TICK, GIN, and EIM confirmed that parasite infestation impacted the performance of animals. Selection for BW under an environment with a controlled parasite burden is an alternative to improve both, BW and HR. There was no impact of age of measurement on the estimates of genetic variance for HR. Five quantitative trait loci (QTL) were associated with HR to EIM but none with HR to TICK and to GIN. These QTL contain genes that were previously shown to be associated with the production of antibody modulators and chemokines that are released in the intestinal epithelium. Selection for BW under natural infestation and controlled parasite burden, via prophylactic parasite control, contributes to the identification of animals that are resilient to nematodes and Eimeria ssp. Although we verified that sufficient genetic variation existed for HR, we did not find any genes associated with mechanisms that could justify the expression of HR to TICK and GIN.
Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein ...(dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs.
ABSTRACT The objective of this study was to estimate the breed, heterosis, and recombination effects on different components of the lactation curve of Girolando cattle. The dataset used consisted of ...12,121 purebred cows of Holstein (H) and Gyr (G) breeds, and six H×G crossbred cows (Girolando). The model used presents random effects of herd and cow, regression coefficient associated with linear effect of proportion of H breed, regression coefficient associated with the linear effect of heterosis between H and G breeds, regression coefficient associated with the linear effect of recombination between H and G breeds, and random effect of residual. Dijkstra's (DJ), Nelder's (ND), Wilmink's (WL), and Wood's (WD) models were tested to fit production records of these different genetic groups. These models were then tested according to evaluation criteria of quality of fit (AIC, BIC, and RMSE), and the two best models (WD and WL) were chosen for estimation of 305-day milk yield (MY305), peak yield, time to peak, and persistency of milk yield. The breed effect was significant for all traits and components of the lactation curve. The heterosis effect was significant for all traits, and was more significant for MY305 (945.62±79.17 kg). Peak yield was the component of lactation curve that presented the most significant heterosis effect, partially explaining the heterosis effect (12 to 21%) found for MY305. The recombination effect was positive only for lactation period and time to peak of lactation in Girolando cows.
Identification of selection signatures in livestock species de Simoni Gouveia, João José; da Silva, Marcos Vinicius Gualberto Barbosa; Paiva, Samuel Rezende ...
Genetics and molecular biology,
06/2014, Letnik:
37, Številka:
2
Journal Article
Recenzirano
Odprti dostop
The identification of regions that have undergone selection is one of the principal goals of theoretical and applied evolutionary genetics. Such studies can also provide information about the ...evolutionary processes involved in shaping genomes, as well as physical and functional information about genes/genomic regions. Domestication followed by breed formation and selection schemes has allowed the formation of very diverse livestock breeds adapted to a wide variety of environments and with special characteristics. The advances in genomics in the last five years have enabled the development of several methods to detect selection signatures and have resulted in the publication of a considerable number of studies involving livestock species. The aims of this review are to describe the principal effects of natural/artificial selection on livestock genomes, to present the main methods used to detect selection signatures and to discuss some recent results in this area. This review should be useful also to research scientists working with wild animals/non-domesticated species and plant biologists working with breeding and evolutionary biology.
The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais-37.5% Zebu) and MA genetic group (MA: 65.6% Charolais-34.4% Zebu) cattle using genomic ...information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle.
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